Question: Memory allocation error
gravatar for Azhar
3.8 years ago by
Azhar50 wrote:

HI I am runnig WGCNA code for calculating co expression adjacency Matrix but I am getting this error I am running this scrip in C directory and it has 60 Gb free space so why it still gives this error

> coexpression<-adjacency(data)
Error: cannot allocate vector of size 28.7 Gb
In addition: Warning messages:
1: In cor(datExpr, use = "p") :
  Reached total allocation of 3810Mb: see help(memory.size)
2: In cor(datExpr, use = "p") :
rna-seq • 1.6k views
ADD COMMENTlink modified 3.8 years ago by WouterDeCoster45k • written 3.8 years ago by Azhar50

The 3810Mb limit it's referring to is RAM, not disk space.

ADD REPLYlink written 3.8 years ago by andrew.j.skelton736.1k

Thanks andrew but what is the mean of

cannot allocate vector size 28.7 Gb

ADD REPLYlink written 3.8 years ago by Azhar50

Hello Azhar!

It appears that your post has been cross-posted to another site:

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 3.8 years ago by WouterDeCoster45k
gravatar for Jean-Karim Heriche
3.8 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche24k wrote:

To be more explicit, it seems you're using a computer with only 4Gb of RAM but your data requires 29 Gb so try running your analysis on a computer with 32 Gb of RAM. Note that if you're using a 32bit version of Windows, you can only use at most 4 Gb even if the computer has more.

ADD COMMENTlink written 3.8 years ago by Jean-Karim Heriche24k
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